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January 2010


FAO International Technical Conference

Agricultural biotechnologies in developing countries: Options and
opportunities in crops, forestry, livestock, fisheries and agro-industry to
face the challenges of food insecurity and climate change (ABDC-10)
Guadalajara, Mexico, 1 4 March 2010
Current status and options for biotechnologies in food processing and in
food safety in developing countries

This background document is the result of the joint effort of many contributors. The initial key
contributions were made by Olusola B. Oyewole from University of Agriculture, Abeokuta, Nigeria
and Ruud Valyasevi from the National Center for Genetic Engineering and Biotechnology (Biotec),
Biotec, Bangkok, Thailand.
Sections relevant to biotechnology applications in food processing: Coordination was done by Rosa
Rolle (Senior Agro-Industries and Post-harvest Officer, FAO Regional Office for Asia and the Pacific)
who also made significant contributions to the document.
Sections relevant to biotechnology applications in food safety: Coordination was done by Masami
Takeuchi (Food Safety Officer, Nutrition and Consumer Protection Division). Significant
contributions were made by Sridhar Dharmapuri, FAO consultant. Technical contributions from
several FAO colleagues, including Maria de Lourdes Costarrica (Senior officer, Nutrition and
Consumer Protection Division) and Annika Wennberg (Senior Officer, FAO JECFA Secretariat,
Nutrition and Consumer Protection Division), to the document are also gratefully acknowledged.
Comments from the following members of the ABDC-10 Steering Committee are gratefully
acknowledged: Adama Diallo (Joint FAO/IAEA Division, Austria), Kathleen Jones (US Food and
Drug Administration, United States), Marci Levine (International Life Sciences Institute, United
States), Haruko Okusu (CGIAR Science Council, Italy), Masashi Kusukawa (Codex Alimentarius
Commission, Italy) and Jrgen Schlundt (World Health Organization, Switzerland). Technical support
and comments from John Ruane and Preet Lidder from the ABDC-10 Secretariat are also gratefully


Table of Contents

Acronyms and abbreviations

A. Introduction
B. Stocktaking - Learning from the Past
1. Biotechnology Definition and scope
2. Current status of the application of traditional and new biotechnologies in food processing in
developing countries
2.1 Methods of microbial inoculation in food fermentations
2.2 Food additives and processing aids
2.3 Current status of the application of traditional and new biotechnologies in food safety and
quality improvement in developing countries
3. Analysis of the reasons for successes/failures of application of biotechnologies in developing
4. Case studies of biotechnology applications in developing countries
4.1 Fermented soy sauce production
4.2 Traditional fermented pork sausage (nham)
4.3 Traditional fermented fish paste Som Fug
4.4 Flavour production from alkaline-fermented beans
C. Looking Forward: Preparing for the Future
5. A key issue in the sector where application of biotechnologies could be useful
6. Identifying options for developing countries
7. Identifying priorities for action for the international community
D. References
E. Glossary of selected terms

Acronyms and Abbreviations

ELISA = Enzyme-linked imumunoabsorbent assay

GC = Gas chromatography
GC/MS = Gas chromatography/mass spectrometry
GHP = Good hygienic practice
GM = Genetically modified
GMO = Genetically modified organism
GMP = Good manufacturing practice
HACCP = Hazard Analysis and Critical Control Point
HPLC = High performance liquid chromatography
IPR = Intellectual property rights
MS = Mass spectrometry
PCR = Polymerase chain reaction
RAPD = Random amplified polymorphic DNA
TLC = Thin layer chromatography

A. Introduction
Food processing makes use of various unit operations and technologies to convert relatively bulky,
perishable and typically inedible raw materials into more useful shelf-stable and palatable foods or
potable beverages. Processing contributes to food security by minimizing waste and losses in the food
chain and by increasing food availability and marketability. Food is also processed in order to improve
its quality and safety. Food safety is a scientific discipline that provides assurance that food will not
cause harm to the consumer when it is prepared and/or eaten according to its intended use. 1
Biotechnology as applied to food processing in most developing countries makes use of microbial
inoculants to enhance properties such as the taste, aroma, shelf-life, texture and nutritional value of
foods. The process whereby micro-organisms and their enzymes bring about these desirable changes
in food materials is known as fermentation. Fermentation processing is also widely applied in the
production of microbial cultures, enzymes, flavours, fragrances, food additives and a range of other
high value-added products. These high value products are increasingly produced in more
technologically advanced developing countries for use in their food and non-food processing
applications. Many of these high value products are also imported by developing countries for use in
their food-processing applications.
This document will discuss the prospects and potential of applying biotechnology in food processing
operations and to address safety issues in food systems with the objective of addressing food security
and responding to changing consumer trends in developing countries. It is important to note that food
safety evaluation or risk assessment will not be discussed here. Instead, this paper will focus on the
context of biotechnologies as applied to food safety.
Technologies applied in the processing of food must assure the quality and safety of the final product.
Safe food is food in which physical, chemical or microbiological hazards are present at a level that
does not present a public health risk. Safe food can, therefore, be consumed with the assurance that
there are no serious health implications for the consumer. Recent food scares such as mad cow disease
and the melamine contamination of food products have increased consumer concern for food safety.
As incomes rise, consumers are increasingly willing to pay a premium for quality, safety and
A range of technologies is applied at different levels and scales of operation in food processing across
the developing world. Conventional or low-input food processing technologies include drying,
fermentation, salting, and various forms of cooking, including roasting, frying, smoking, steaming,
and oven baking. Low-income economies are likely to employ these as predominant technologies for
the processing of staple foods. Many of these technologies make use of a simple, often rudimentary,
technological base. Medium levels of processing technologies such as canning, oven drying, spray
drying, freeze drying, freezing, pasteurization, vacuum packing, osmotic dehydration and sugar
crystallization are widely applied in middle- and upper middle-income economies. Higher-level, more
capital-intensive food-processing technologies such as high-temperature short-time pasteurization and
high-pressure low-temperature food processing are widely employed in middle- and upper middleincome economies. Functional additives and ingredients produced using fermentation processes are
generally incorporated into food-processing operations that make use of higher-level technologies.
Traditional methods of food-safety monitoring such as the detection of pathogenic bacteria in food are
generally based on the use of culture media. These are the techniques of choice in low- and lowermiddle-income economies which lack the resources, infrastructure and technical capacity to utilize

1. Recommended International Code of Practice General Principles of Food Hygiene (Codex Alimentarius
Commission, 2009)

modern biotechnological techniques. Conventional bacterial detection methods are time-consuming
multi-step procedures. At least two to three days are required for the initial isolation of an organism,
followed by the requirement for several days of additional confirmatory testing. Biotechnology-based
methods can provide accurate results within a relatively short time frame. Biotechnological
developments have resulted in the widespread availability of low-cost rapid methods of identification
when compared with the significant cost/time requirements of conventional techniques. Lowermiddle-income economies apply both traditional and more sophisticated methods for monitoring the
microbiological quality of foods and their conformance to international standards.
A number of case studies are described in the text to demonstrate the utility of biotechnology-based
applications in food processing and food safety. These case studies provide the basis for the
development of strategic interventions designed to upgrade food processing and food safety in
developing countries through the application of biotechnology.
This paper is divided into two main parts Stocktaking: Lessons from the past and Looking forward:
preparing for the future. Within the context of Stocktaking, Section 1 provides a brief definition of
biotechnologies. This is followed by an overview of the current status of the application of
biotechnologies, both traditional and new, in developing countries (Section 2). Section 3 provides an
analysis of the successes/failures of the application of biotechnologies in developing countries and
underlying causative factors, while some case studies of applications in developing countries are
provided in Section 4. The Looking forward part comprises the next three sections (5-7). Section 5
deals with a key issue in the sector where the application of biotechnologies might be useful. Section 6
proposes options for developing countries to make informed decisions about the application of
appropriate biotechnologies, and Section 7 presents priorities for action for the international

B. Stocktaking - Learning from the Past

1. Biotechnology Definition and scope
For the purpose of this paper, biotechnology is defined in accordance with the Convention on
Biological Diversity, i.e. "any technological application that uses biological systems, living
organisms, or derivatives thereof, to make or modify products or processes for specific use. .
Biotechnology in the food processing sector makes use of micro-organisms for the preservation of
food and for the production of a range of value-added products such as enzymes, flavour compounds,
vitamins, microbial cultures and food ingredients. Biotechnology applications in the food-processing
sector, therefore, target the selection and manipulation of micro-organisms with the objective of
improving process control, product quality, safety, consistency and yield, while increasing process
Biotechnological processes applicable to the improvement of microbial cultures for use in foodprocessing applications include traditional methods of genetic improvement (traditional
biotechnology) such as classical mutagenesis and conjugation. These methods generally focus on
improving the quality of micro-organisms and the yields of metabolites. Hybridization is also used for
the improvement of yeasts involved in baking, brewing and in beverage production. Saccharomyces
cerevisiae strains have, for example, been researched for improved fermentation, processing and
biopreservation abilities, and for capacities to increase the wholesomeness and sensory quality of wine
(Pretorius and Bauer, 2002). Methods employed in the genetic research and development of wine
yeasts are summarized in Table 1.
Recombinant gene technology, the best-known modern biotechnology, is widely employed in research
and development for strain improvement. The availability of genetic manipulation tools and the
opportunities that exist to improve the microbial cultures associated with food fermentations are
tempered by concerns over regulatory issues and consumer perceptions. Genetically modified (GM)
microbial cultures are, however, used in the production of enzymes and various food-processing
ingredients such as monosodium glutamate, polyunsaturated fatty acids and amino acids.
Biotechnology is also widely employed as a tool in diagnostics in order to monitor food safety,
prevent and diagnose food-borne illnesses and verify the origins of foods. Techniques applied in the
assurance of food safety focus on the detection and monitoring of hazards whether biological,
chemical or physical. These applications will be explored and discussed in subsequent sections.
2. Current status of the application of traditional and new biotechnologies in food processing in
developing countries
2.1 Methods of microbial inoculation in food fermentations
The fermentation bioprocess is the major biotechnological application in food processing. It is often
one step in a sequence of food-processing operations, which may include cleaning, size reduction,
soaking and cooking. Fermentation bioprocessing makes use of microbial inoculants for enhancing
properties such as the taste, aroma, shelf-life, safety, texture and nutritional value of foods. Microbes
associated with the raw food material and the processing environment serve as inoculants in
spontaneous fermentations, while inoculants containing high concentrations of live micro-organisms,
referred to as starter cultures, are used to initiate and accelerate the rate of fermentation processes in
non-spontaneous or controlled fermentation processes. Microbial starter cultures vary widely in
quality and purity.

Starter culture development and improvement is the subject of much research both in developed and in
developing countries. While considerable work on GM starter culture development is ongoing at the
laboratory level in developed countries, relatively few GM micro-organisms have been permitted in
the food and beverage industry globally. In 1990, the United Kingdom became the first country to
permit the use of a live genetically modified organism (GMO) in food. It was a bakers yeast,
engineered to improve the rate at which bread dough rises by increasing the efficiency with which
maltose is broken down. This modification was done by using genes from yeast and placing them
under a strong constitutive promoter. The United Kingdom has also approved a GM brewers yeast for
beer production. By introducing a gene encoding glucoamylase from yeast, better utilization of
carbohydrate present in conventional feedstock can be obtained, resulting in increased yields of
alcohol and the ability to produce a full-strength, low-carbohydrate beer. More recently, two
genetically modified yeast strains were authorized for use in the North American wine industry (Bauer
et al., 2007).
Current literature documents volumes of research reports on the characterization of microbes
associated with the production of traditional fermented foods in developing countries. Relatively few
of these studies document the application of the diagnostic tools of modern biotechnology in
developing and designing starter cultures. The development and improvement of microbial starters has
been a driving force for the transformation of traditional food fermentations in developing countries
from an art to a science. Microbial starter culture development has also been a driving force for
innovation in the design of equipment suited to the hygienic processing of traditional fermented foods
under controlled conditions in many developing countries.
Starter culture improvement, together with the improvement and development of bioreactor
technology for the control of fermentation processes in developed countries, has played a pivotal role
in the production of high-value products such as enzymes, microbial cultures, and functional food
ingredients. These products are increasingly produced in more advanced developing economies, and
are increasingly imported by less advanced developing countries, as inputs for their food processing
a) Spontaneous inoculation of fermentation processes
In many developing countries, fermented foods are produced primarily at the household and village
level, using spontaneous methods of inoculation. Spontaneous fermentations are largely uncontrolled.
A natural selection process, however, evolves in many of these processes which eventually results in
the predominance of a particular type or group of micro-organisms in the fermentation medium. A
majority of African food-fermentation processes make use of spontaneous inoculation (Table 2).
Major limitations of spontaneous fermentation processes include their inefficiency, low yields of
product and variable product quality. While spontaneous fermentations generally enhance the safety of
foods owing to a reduction of pH, and through detoxification, in some cases there are safety concerns
relating to the bacterial pathogens associated with the raw material or unhygienic practices during
b) Appropriate starter cultures as inoculants of fermentation processes
Appropriate starter cultures are widely applied as inoculants across the fermented food sector, from
the household to industrial level in low-income and lower-middle-income economies. These starter
cultures are generally produced using a backslopping process which makes use of samples of a
previous batch of a fermented product as inoculants (Holzapfel, 2002). Appropriate starter cultures are
widely applied in the production of fermented fish sauces and fermented vegetables in Asia (Table 3)
and in cereal or grain fermentations in African and Latin American countries (Tables 2 and 4). The
inoculation belt (Holzapfel, 2002) used in traditional fermentations in West Africa serves as a carrier
of undefined fermenting micro-organisms, and is one example of an appropriate starter culture. It
generally consists of a woven fibre or mat or a piece of wood or woven sponge, saturated with high7

quality product of a previously fermented batch. It is immersed into a new batch, in order to serve as
an inoculant. The inoculation belt is used in the production of the indigenous fermented porridges,
uji and mawe, as well as in the production of the Ghanaian beer, pito (Table 2).
Iku, also referred to as iru, is yet another example of an appropriate starter culture produced by
backslopping. This starter culture is produced from concentrated fermented dawadawa (a fermented
legume product), mixed with ground unfermented legumes, vegetables such as pepper, and cereals,
such as ground maize. It is stored in a dried form and is used as an inoculant in dawadawa
fermentations in West Africa (Holzapfel, 2002).
A range of appropriate starter cultures, either in a granular form or in the form of a pressed cake is
used across Asian countries as fermentation inoculants. These traditional mould starters are generally
referred to by various names such as marcha or murcha in India, ragi in Indonesia, bubod in the
Philippines, nuruk in Korea, koji in Japan, ragi in Malaysia and Loog-pang in Thailand. They
generally consist of a mixture of moulds grown under non-sterile conditions.
c) Defined starter cultures as inoculants of fermentation processes
Few defined starter cultures have been developed for use as inoculants in commercial fermentation
processes in developing countries. Nevertheless, the past ten years have witnessed the development
and application of laboratory-selected and pre-cultured starter cultures in food fermentations in a few
developing countries. These developments have taken place primarily in Asian countries (Table 3).
Defined starter cultures consist of single or mixed strains of micro-organisms (Holzapfel 2002).
They may incorporate adjunct culture preparations that serve a food-safety and preservative function.
Adjunct cultures do not necessarily produce fermentation acids or modify texture or flavour, but are
included in the defined culture owing to their ability to inhibit pathogenic or spoilage organisms. Their
inhibitory activity is due to the production of one or several substances such as hydrogen peroxide,
organic acids, diacetyl and bacteriocins (Hutkins, 2006).
By and large, defined cultures are produced by pure culture maintenance and propagation under
aseptic conditions. They are generally marketed in a liquid or powdered form or else as a pressed cake.
Loog-pang, a defined culture marketed in Thailand in the form of a pressed rice cake, consists of
Saccharomyces cerevisiae, Aspergillus oryzae or Rhizopus sp. and Mucor. Loog-pang has a shelf life
of 23 days at ambient temperature and 57 days under refrigerated conditions. Ragi cultures are
commercially produced by the Malaysian Agricultural Research and Development Institute by mixing
a culture inoculum which generally consists of Rhizopus Oligosporus with moistened sterile rice flour,
and incubating it at ambient temperature for four days. This starter has a shelf life of two weeks under
refrigerated conditions (Merican and Quee-Lan, 2004). It is widely used as an inoculant in the
production of traditional Malaysian fermented foods. Ragi-type starter cultures for the production of a
range of fermented Indonesian products such as oncom, tape and tempeh are currently marketed via
the internet.
Defined starter cultures are also widely imported by developing countries for use in the commercial
production of dairy products such as yogurt, kefir, cheeses and alcoholic beverages. Many of these
cultures are tailored to produce specific textures and flavours. In response to growing consumer
interest in attaining wellness through diet, many yogurt cultures also include probiotic strains.
Probiotics are currently produced in India for use as food additives, dietary supplements and for use in
animal feed (e.g. Methodologies used in the
development and tailoring of these starters are largely proprietary to the suppliers of these starters.
Monosodium glutamate and lactic acid, both of which are used as ingredients in the food industry, are
produced in less-advanced developing countries using defined starter cultures.
d) Defined starter cultures developed using the diagnostic tools of advanced biotechnologies

The use of DNA-based diagnostic techniques for strain differentiation can allow for the tailoring of
starter cultures to yield products with specific flavours and/or textures. Random amplified
polymorphic DNA (RAPD) techniques have been applied in, for example, Thailand, in the molecular
typing of bacterial strains and correlating the findings of these studies to flavour development during
the production of the fermented pork sausage, nham (see Case Study 4.2). The results of these
analyses led to the development of three different defined starter cultures which are currently used for
the commercial production of products having different flavour characteristics (Valyasevi and Rolle,
e) GM starter cultures
To date, no commercial GM micro-organisms that would be consumed as living organisms exist.
Products of industrial GM producer organisms are, however, widely used in food processing and no
major safety concerns have been raised against them. Rennet which is widely used as a starter in
cheese production across the globe is produced using GM bacteria. These are discussed in more
specific detail in Section 2.2. Thailand currently makes use of GM Escherichia coli as an inoculant in
lysine production. Many industrially important enzymes such as -amylase, gluco-amylase, lipase and
pectinase and bio-based fine chemicals, such as lactic acid, amino acids, antibiotics, nucleic acid and
polysaccharides, are produced in China using GM starter cultures. Other developing countries which
currently produce enzymes using recombinant micro-organisms include Cuba, Brazil, India, and
2.2 Food additives and processing aids
Enzymes, amino acids, vitamins, organic acids, polyunsaturated fatty acids and certain complex
carbohydrates and flavouring agents used in food formulations are currently produced using GM
micro-organisms. Examples of some of these products are listed in Table 5.
Enzymes occur in all living organisms and catalyze biochemical reactions that are necessary to support
life (Olempska-Beer et al. 2006). They are commonly used in food processing and in the production of
food ingredients. The use of recombinant DNA technology has made it possible to manufacture novel
enzymes that are tailored to specific food processing conditions. Alpha amylases with increased heat
stability have, for example, been engineered for use in the production of high-fructose corn syrups.
These improvements were accomplished by introducing changes in the -amylase amino acid
sequences through DNA sequence modifications of the -amylase genes (Olempska-Beer et al. 2006).
Bovine chymosin used in cheese manufacture was the first recombinant enzyme approved for used in
food by the US Food and Drug Administration (Flamm, 1991). The Phospholipase A1 gene from
Fusarium venenatum is expressed in GM Aspergillus oryzae to produce the phospholipase A1 enzyme
used in the dairy industry for cheese manufacture to improve process efficiencies and cheese yields.
Considerable progress has been made in recent times toward the improvement of microbial strains
used in the production of enzymes. Microbial host strains developed for enzyme production have been
engineered to increase enzyme yields by deleting native genes encoding extracellular proteases.
Certain fungal producing strains have also been modified to reduce or eliminate their potential for
producing toxic metabolites (Olempska-Beer et al., 2006). Enzymes derived from recombinant microorganisms are listed in Table 6.
Enzymes used in food processing have historically been considered non-toxic. Some characteristics
arising from their chemical nature and source, such as allergenicity, activity-related toxicity, residual
microbiological activity and chemical toxicity are, however of concern. These attributes of concern
must, however, be addressed in light of the growing complexity and sophistication of the
methodologies used in the production of food-grade enzymes. Safety evaluation of all food enzymes,
including those produced by GM micro-organisms, is essential if consumer safety is to be assured

(Spok, 2006). Enzymes produced using GM micro-organisms wherein the enzyme is not part of the
final food product have specifically been evaluated by the Joint FAO/WHO Expert Committee on
Food Additives (JECFA). Safety evaluations have been conducted using the general specifications and
considerations for enzyme preparations used in food processing (FAO, 2006). Preparations of
asparaginase enzymes have also been evaluated by JECFA (Olempska-Beer, 2008).
Flavours, amino acids and sweeteners
Volatile organic chemicals such as flavours and aromas are the sensory principles of many consumer
products and govern their acceptance and market success (Berger, 2009). Flavours produced using
micro-organisms currently compete with those from traditional agricultural sources. According to
Berger (2009), more than 100 commercial aroma chemicals are derived using biotechnology either
through the screening for overproducers, the elucidation of metabolic pathways and precursors or
through the application of conventional bioengineering. Recombinant DNA technologies have also
enhanced efficiency in the production of non-nutritive sweeteners such as aspartame and thaumatin.
Market development has been particularly dynamic for the flavour enhancer glutamate
(Leuchtenberger, Huthmacher and Drauz, 2005) which is produced by the fermentation of sugar
sources such as molasses, sucrose or glucose using high-performance strains of Corynebacterium
glutamicum and Escherichia coli. Amino acids produced through biotechnological processes are also
of great interest as building blocks for active ingredients used in a variety of industrial processes.
2.3 Current status of the application of traditional and new biotechnologies in food safety and in
quality improvement in developing countries
Food safety issues and concerns in food fermentation processing
Microbial activity plays a central role in food fermentation processes, resulting in desirable properties
such as improvements in shelf-life and quality attributes such as texture and flavour. Pathogenic
organisms are, however, of prime concern in fermented foods. Anti-nutritional factors such as
phytates, tannins, protein inhibitors, lectins, saponins, oligosaccharides and cyanogenic glucosides are
naturally occurring components of raw materials commonly used in food fermentations in developing
countries. Contamination of the fermentation process can pose a major health risk in the final
fermented product. Methodologies for identifying and monitoring the presence of chemical (pesticide
residues, heavy metals, trace elements) and biochemical (aflatoxins) hazards in fermented foods are,
therefore, a critical need. Furthermore, with growing consumer interest in the credence attributes of
the products that they consume, and the premium currently being placed on quality linked to
geographical origin, the traceability of foods with selected properties is of increasing importance.
Advances in microbial genetics
In recent times, the genetic characterization of micro-organisms has advanced at a rapid pace with
exponential growth in the collection of genome sequence information, high-throughput analysis of
expressed products i.e., transcripts and proteins and the application of bioinformatics which allows
high throughput comparative genomic approaches that provide insights for further functional studies.
Genome sequence information, coupled with the support of highly advanced molecular techniques,
have allowed scientists to establish mechanisms of various host-defensive pathogen counter-defensive
strategies and have provided industry with tools for developing strategies to design healthy and safe
food by optimizing the effect of probiotic bacteria, the design of starter culture bacteria and functional
properties for use in food processing. Characterization of the genomes of lactic acid probiotics has, for
example, shed light on the interaction of pathogens with lactic acid bacteria (de Vos, 2001).
Nucleotide sequences of the genomes of many important food microbes have recently become
available. Saccharomyces cerevisiae was the first food microbe for which a complete genome
sequence was characterized (Goffeau et al., 1996). This was followed by genome sequencing of the
related yeast, Kluyveromyces lactis (Bolotin-Fukuhara et al., 2000) as well as filamentous fungi which
are major enzyme producers and have significant applications in the food-processing industry.

Genome nucleotide sequences of many Gram-positive bacteria species have also been completed. The
Bacillus subtilis genome was the first to be completed, followed by that of the Lactococcus lactis
genome. Genome sequences of food-borne pathogens such as Campylobacter jejuni (Parkhill et al.,
2000), verocytotoxigenic Escherichia coli O157:H7 (Hayashi et al., 2001) and Staphylococcus aureus
(Kuroda et al., 2001) have also been completed. Genome sequences of microbes that are of importance
in food processing, such as Lactobacillus plantarum (Zhang et al., 2009) are also available. The
genome of Clostridium botulinum, responsible for food poisoning, was also recently completed
(Sanger Institute, 2009).
Detection of pathogens
The rapid detection of pathogens and other microbial contaminants in food is critical to assess the
safety of food products. Traditional methods to detect food-borne bacteria often rely on timeconsuming growth in culture media, followed by isolation, biochemical identification, and sometimes
serology. Recent technological advances have improved the efficiency, specificity and sensitivity of
detecting micro-organisms. Detection technologies employ the polymerase chain reaction (PCR)
assay. Short fragments of DNA (probes) or primers are hybridized to a specific sequence or template,
which is subsequently enzymatically amplified by the Taq polymerase enzyme using a thermocycler
(Barrett, Fang and Swaminathan, 1997). In theory, a single copy of DNA can be amplified a millionfold in less than 2 hours with the use of PCR techniques; hence, the potential of PCR to eliminate or
greatly reduce the need for cultural enrichment. The genetic characterization of genome sequence
information has further facilitated the identification of virulence nucleotide sequences for use as
molecular markers in pathogen detection. Multiplex real-time PCR methods are now available to
identify the E. coli O157:H7 serogroup (Yoshitomi, Jinneman and Weagan, 2003). PCR-based
identification methods are also available for Vibrio cholerae (Koch, Payne and Cebula, 1995) and for
major food-related microbes such as Campylobacter jejuni, C. coli, Yersinia enterocolitica, Hepatitis
A virus, Salmonella, Staphylococcus aureus (Bacteriological Analytical Manual, 2003).
Sophisticated cultural media such as chromogenic or fluorogenic media are not readily used in lowincome economies but are relatively widespread in lower-middle-income and upper-middle-income
economies. The use of immunoassays such as enzyme-linked immunosorbent assay (ELISA) is also
very limited in low-income economies but is more widespread in the form of diagnostic kits in lowermiddle and upper-middle-income economies. DNA methods, which require elaborate infrastructure
and high technical competence, find minimal application in lower-income and some lower-middleincome economies. Biotechnologies applied in food safety assays in developing countries are
summarized in Table 7.
There are movements toward implementing safety-control programmes such as the application of
Hazard Analysis and Critical Control Point (HACCP) in food fermentations in many developing
countries. A HACCP plan for the production of the Thai fermented meat product is summarized in
Table 8. The application of HACCP necessitates the deployment of good agricultural practices, good
manufacturing practices (GMPs) and good hygienic practices (GHPs) and the monitoring of critical
control points for potential microbial and chemical contamination during bioprocessing (FAO, 1995).
Rigorous adherence to sanitary practices in the processing environment necessitates rapid, dynamic,
sensitive, specific as well as versatile and cost-effective assay methods. The molecular approach of
biotechnology entails near-time or real-time bacterial detection, and offers sensitivity and specificity
unchallenged by traditional/conventional methods.
Mycotoxin detection
The problem of mycotoxin contamination in food including fermented foods is a global concern.
Mycotoxin contamination is particularly prevalent in developing countries in tropical areas such as in
South Asia and Africa. High-performance liquid chromatography (HPLC) and gas
chromatography/mass spectrometry (GC/MS) are two of the most widely used methods for the
detection and quantification of mycotoxins in developing countries. These methods, however, are
time-consuming, difficult to use and require laboratory facilities. Immunoassays that are economical in

use, sensitive and easy to use would greatly facilitate the detection and quantization of mycotoxins. A
number of ELISA kits are now commercially available for the detection of aflatoxins, deoxynivalenol,
fumonisins, ochratoxins, and zearalenone (Schmale and Munkvold, 2009).
Detection and identification of foods and food ingredients
The DNA-based identification code system is reliant on polymorphisms at the nucleotide level for the
differentiation of living organisms at the variety and species levels. Currently PCR-based methods are
used either for the purpose of detecting single nucleotide polymorphisms (SNPs) giving rise to
restriction fragment length polymorphisms (RFLPs) or for detecting small sequence length
polymorphisms (SSLPs) often known as Variable Number Tandem Repeats (VNTRs). These methods
facilitate the identification of unique polymorphisms of a variety of food commodities and can be used
in the identification of their source or origin. These unique polymorphisms are often referred to as
DNA barcodes (Teletchea, Maudet and Hnni, 2005). The DNA barcode is used for the identification
of specific varieties in food detection and in food traceability. The DNA barcode has been used for the
identification of many products for export in countries such as Thailand, China, Brazil, Cuba and
Argentina, The DNA barcode of microsatellite markers has also been successfully used in
differentiating and identifying fermented products such as premium wines, cheeses and sausages on
the basis of their origins. Basmati rice varieties and olive cultivars used in olive oil production (Sefc et
al., 2000) have also been differentiated.
3. Analysis of the reasons for successes/failures of application of biotechnologies in developing
Socio-economic factors have played a major role in the adoption and application of microbial
inoculants in food fermentations. In situations where the cost of food is a major issue, uptake and
adoption of improved biotechnologies has been generally slow. Demand for improved inoculants and
starter culture development has been triggered by increasing consumer income, education and new
market opportunities.
3.1 Socio-economics of the consumer base
The consumer base of traditionally fermented staple foods in most developing countries is largely poor
and disadvantaged. Price, rather than food safety and quality, is therefore a major preoccupation of this
group when purchasing food. Fermented foods provide that target group with an affordable source of
food, and make a substantial contribution to their food and nutritional security. These foods are
generally produced under relatively poor hygienic conditions at the household and village level.
Fermentation processing is practised largely as an art in such contexts.
Interventions designed to upgrade processes used in the production of these traditionally fermented
staples have been largely carried out through donor-funded projects and have focused primarily on
reducing the drudgery associated with the fermentation processes. Improvements have also targeted
the upgradation of hygienic conditions of fermentation processes and the introduction of simple and
appropriate methodologies for the application of inoculants, such as the use of backslopping. While
the uptake of simple backslopping technologies at the household level has, in general, been very good
by that target group, the uptake of defined starter cultures has been less successful, owing to cost
considerations. Case Study 4.3 on the household level production of Som Fug in Thailand highlights
the poor uptake of improved starter culture technologies by household-level processors, primarily on
the basis of cost.
With growing incomes and improved levels of education in urban centres across a number of
developing countries, dietary habits are changing and a wider variety of foods is being consumed.
Fermented foods are no longer the main staples, but are still consumed as side dishes or condiments by
that target group. The demand of that target group for safe food of high quality has begun to re-orient
the traditional fermented food sector, and led to improvements in the control of fermentation processes

through the development and adoption of defined starter cultures, the implementation of GHPs and
HACCP in food fermentation processing, and the development of bioreactor technologies, coupled
with appropriate downstream processing to terminate fermentation processes and thus extend the
shelf-life of fermented foods. The packaging of fermented products has also improved. Case Study 4.1
on soy sauce production in Thailand highlights an example of how starter culture development
coupled with bioreactor technology has improved yields and the efficiency of fermentation processes,
while Case Study 4.2 highlights how consumer demand for safe food led to research and development
into starter culture development designed to improve the safety of nham in the marketing chain.
3.2 Changing consumer demand trends
Apart from their changing dietary patterns and their demand for safety and quality, higher-income
consumers demand convenience and are increasingly concerned about deriving health benefit from the
foods they consume. Many of these consumers also show a preference for shopping in supermarkets.
Consumer demand for deriving wellness through food consumption has stimulated the development of
industrial fermentation processes for the production of functional ingredients such as polyunsaturated
fatty acids and pro-biotic cultures for use as food ingredients in developing countries. These functional
ingredients are currently applied in the fortification of fermented foods as well as in the production of
dietary supplements in countries such as India.
The growth of supermarkets in developing countries has promulgated the need for standardized
products of a reasonable shelf-life that meet safety and quality criteria. Packaged fermented products
such as kimchi, miso and tempeh, for example, are widely available in supermarkets across Asia. The
production of traditional beer in a powdered format and in ready-to-drink containers in Zambia is a
very good example of product development that has taken place in response to consumer demand for
convenience, both in local and export markets.
Shifting consumer preferences in South Africa, away from basic commodity wine to top-quality wine,
is yet another example of how market demand has led to research and biotechnological innovation in
the wine industry. Biotechnological innovations in that country are currently focused on the
improvement of Saccharomyces cerevisiae strains to improve wholesomeness and sensory quality of
3.3 The enabling environment for starter culture development
A considerable amount of research in developing countries has focused on the identification of starter
micro-organisms associated with the fermentation of these staple foods. The greatest strides in starter
culture development have, however, been realized in countries that have prioritized the development
of technical skills, the infrastructural support base and funding support for research into the
upgradation of fermentation processes. Linkages between research institutions and the manufacturing
sector have also been critical to the successful introduction of starter cultures. Case Study 4.1 on soy
sauce production exemplifies how success was achieved through such collaboration. Case Study 4.2
on nham production in Thailand also highlights how collaboration between the manufacturing sector
and public sector research institutions resulted in the development of improved starter cultures and the
uptake of these cultures by nham manufacturers to assure product safety.
Collaborative initiatives among research institutions have also had a major positive impact on
biotechnological developments in developing countries. Collaboration among African institutions and
their counterparts in the North has greatly facilitated improvements in biotechnological research and
capacity development in the area of food biotechnology on the continent. One major success story in
this regard has been collaborative projects involving Burkina Faso, Ghana and institutions in the
Netherlands. This programme facilitated the typing and screening of microbial cultures associated
with fermented African foods as a basis for starter culture development. Results of this work (Mengu,

2009) led to improvements in the production of gari, a fermented cassava product and dawadawa, a
fermented legume product.
Issues related to the protection of intellectual property rights (IPR) are of growing concern with
respect to starter culture development. Case Study 4.4, describing flavour production using alkalinefermented beans, highlights the critical importance of IPR referring to processes applied in the
production of traditional fermented foods.
3.4 Proactive industrial strategies
Biotechnology developments have been most successful in areas where proactive approaches are taken
by industry. The Thai food industry successfully creates perceived quality by launching new product
logos and associating these new products with biotechnology or with the fact that they were developed
using traditional biotechnology, such as starter cultures. The goal of the industry is to project an image
of itself as producing products of superior quality and safety that represent progressiveness based on a
higher level of technology.
3.5 Export opportunities for fermented products
Increasing travel due to globalization has changed the eating habits of consumers across the globe.
Export markets for fermented foods have grown out of the need to meet the requirements of
developing country diaspora in these markets as well as to satisfy growing international demand for
niche and ethnic products. Indonesian tempe and Oriental soy sauce are well known examples of
indigenous fermented foods that have been industrialized and marketed globally. The need to assure
the safety and quality of these products in compliance with requirements of importing markets has
been a driving force for the upgrading of starter cultures as well as for diagnostic methodologies for
verification of their quality and safety.
Growing interest and trade in fermented food products is also likely to lead to the greater use of the
DNA barcode for identifying the origins of specific fermented food products produced in developing
4. Case studies of applications of biotechnologies in developing countries
4.1 Fermented soy sauce production
This Case Study on the production of soy sauce highlights success in the application of starter culture
technology and the use of improved bioreactor technology. It exemplifies the transition of a craftbased production system to a technology-based production system. Research leading to these
developments was supported by an international organization, followed by funding support from the
Government of Thailand and the Thai soy sauce industry. Developments of the process were largely
driven by the demand pull created by a soy sauce industry consortium in Thailand in order to meet
market requirements.
Soy sauce production involves a two-step fermentation process that makes use of koji inoculants in the
initial phase, followed by moromi inoculants in the second phase. The initial phase of the fermentation
involves the soaking of soybeans in water for 12 hours, boiling for approximately 17 hours to
hydrolyze the protein complex, and the addition of the koji culture Aspergillus oryzae for proteolysis
of the soy proteins. Using this traditional method of production, the process of proteolysis takes
between 40 hours and seven days depending on the method and the conditions used. The second phase
of the fermentation process, which is referred to as a moromi fermentation, involves the addition of
brine solution to the koji. Saccharomyces rouxii, a salt-tolerant yeast, is the predominant microorganism in this phase of the fermentation, which lasts as long as 812 months. Moromi fermentations
are traditionally conducted in earthenware jars, which often poses a limitation to the manufacturers

both in terms of expansion and in terms of production capacity (Valyasevi and Rolle, 2002). The soy
sauce industry has moved up the ladder of development, from an art to a technology-based process
through the introduction of defined starter cultures and improvements in the control of the
fermentation process. Physical and biological parameters of the fermentation process are controlled
through the use of koji and moromi cultures and koji and moromi fermentors.
Use of the koji starter, Aspergillus flavus var. Columnaris, was found to enhance product safety and
uniformity. The introduction of pressure cookers as an innovation for hydrolyzing the soybeans
reduced the time required for solubilization from 17 hours to 2.5 hours. Moreover, the use of starter
culture technology facilitated the development of fermentation chambers with controlled temperature
and humidity conditions, which resulted in shortening the duration of the fermentation process. The
resulting soy sauce had a higher (6%) soluble protein content than that derived from boiled soybeans.
These developments resulted in economic gain for the soy sauce industry and greater value added to
the product in terms of quality and safety
4.2 Traditional fermented pork sausage (nham)
Nham is an indigenous fermented pork sausage produced in Southeast Asia. It is prepared from ground
pork, pork rinds, garlic, cooked rice, salt, chili, sugar, pepper and sodium nitrite.
This Case Study on nham demonstrates how consumer demand for safe food resulted in the
commercial use of defined starter cultures, with the collaboration and support of government agencies.
The diagnostic role of biotechnology in starter culture development for the tailor making of cultures is
also highlighted.
Nham is traditionally consumed as a condiment in the uncooked state in Thailand. It is generally
produced using a uncontrolled fermentation process. Fermentation of the product occurs during
transportation from the manufacturer to the point of retail. The product is generally retailed under
ambient conditions. Traditionally produced nham is considered high risk by Thai health authorities,
who require a warning label stating that the product must be cooked before consumption on the
The first step in the transition to science-based technology for nham fermentations was the
development of a starter culture. This starter was subsequently adopted by a nham manufacturer who
also implemented HACCP in his operation in order to assure safety and to satisfy the compulsory
standard requirements of GMP in the food processing industry imposed by the Thai Food and Drug
Administration. A microbiological hazard profile was developed for nham by the manufacturer in
collaboration with scientists from the Ministry of Science, who established that the prevalent
pathogens in nham were Salmonella spp. (16%), Staphylococcus aureus (15%) and Listeria
monocytogenes (12%) (Paukatong and Kunawasen, 2001). Nitrite, an additive used in nham
production was identified as a chemical hazard and the metal clips used for closure of the package
were identified as physical hazards. A HACCP plan which included four critical control points was
developed for nham (Table 8).
The critical control point on nitrite was monitored by checking the pre-weighed nitrite prior to adding
it to the product formulation. Scientific data generated through the conduct of studies on starter
cultures showed that a rapid increase in acidity within 3648 hours of fermentation inhibited the
growth of bacterial pathogens such as Staphylococcus aureus and Salmonella spp. (Paukatong and
Kunawasen, 2001; Chokesajjawatee et al., 2009). With the application of these starter cultures, the
final product was sent to retailers after the fermentation reached its end-point (pH< 4.5). An
innovative pH indicator which undergoes a colour change on attainment of the end-point of the
fermentation process (pH<4.5) was included in the package. With these innovations and the
implementation of a HACCP plan, local health authorities waived the requirement for the warning
must cook before consumption on the package. This authorization was seen by the public as an
endorsement of product quality and safety by the health authority. Subsequent to these developments,

three medium-sized manufacturers followed suit in adopting the improved technology. Recognition of
the starter culture technology as a food safety measure by the health authority was, of itself, an
effective public awareness campaign.
RAPD markers were used for the molecular typing of approximately 100 bacterial strains at 12-hour
intervals during nham fermentations. These studies resulted in the development and commercialization
of three different starter formulae for use by larger manufacturers of nham. These starter cultures are
marketed in a liquid form which requires refrigeration. Dried starter cultures have a shelf life of one
month at ambient temperature. Further innovations have led to the incorporation of local yeast extracts
into starter culture development, resulting in a 20- to 30-fold reduction in cost. The adoption of starter
culture technology in nham fermentations has had a positive impact on the industry in terms of safety
assurance to consumers and product consistency.
4.3 Traditional fermented fish paste Som Fug
Som Fug is a traditional fermented minced fish cake. It is considered a healthy and highly nutritious
product, and is an excellent source of protein (protein content: 15.7%, fat: 3.2% and total
carbohydrates: 4%). It is produced using a spontaneous microbial fermentation process similar to that
used for producing nham and many other Southeast Asian fermented foods. This Case Study
demonstrates that the uptake and use of starter culture technologies is still largely contingent on cost
considerations and consumer appreciation of the nutritional value of the product.
Compositionally, Som Fug consists of minced freshwater fish (mud carp, Cirrhina microlepis) 84%
(w/w), garlic 8%, water 4%, salt 2%, boiled rice 1%, sucrose 0.1% and black pepper. It is fermented
for about 24 days at ambient temperature. Lactic acid bacteria are the dominant microflora (PaludanMuller, Huss and Gram, 1999) associated with the fermentation. RAPD-PCR analyses determined that
the garlic fermenting lactic acid bacteria associated with Som Fug fermentations belonged to
Lactobacillus pentosus and Lact. plantarum (Paludan-Muller et al., 2002). Furthermore, the studies
also concluded that fructans from garlic are important carbon sources which catalyze the fermentation
of Som Fug. The studies of Som Fug illustrate the high discriminatory power of biotechnology in
differentiating lactic acid bacteria at the strain level. The Som Fug industry did not see the benefit of
implementing starter-culture technology. Although the important micro-organisms for Som Fug
fermentation had been identified, there were no attempts to develop starter cultures. One major reason
for the lack of development of starter-culture technology was the widespread production of Som Fug
at the household level. Household manufacturers do not see the benefit of starter-culture technology
but, rather, view starter cultures as a burden to the cost of production. Moreover, there is no scientific
information to substantiate the nutritional value of Som Fug and hence there is very little public
awareness of the nutritional value of the product.
4.4 Flavour production from alkaline-fermented beans
This Case Study on the indigenous fermentation of the locust bean, dawadawa (fermented locust
bean), is a classic example of how traditional fermentations can be exploited for the production of
high-value products such as flavour compounds. The work, however, was undertaken by a large
cooperation with little involvement of local researchers. Returns on commercial successes derived
from this study did not go back to the people who invented the traditional method of producing this
indigenous fermented food. This Case Study, therefore, serves to highlight the critical issue of IPR of
traditional production systems.
Dawadawa is produced by alkaline fermentation of the African fermented locust bean (Steinkraus,
1995). It is an important condiment in the West/Central African Savannah region (Odunfa and
Oyewole, 1986). Similar fermented food products can be found throughout Africa, with regional
differences in the raw materials used as processing inputs or in postprocessing operations. Similarly
fermented products are referred to as kinda in Sierra Leone, iru in coastal Nigeria, soumbara in

Gambia and Burkina Faso, and kpalugu in parts of Ghana (Odunfa and Oyewole, 1986). Foods
produced by alkaline fermentation in other parts of the world include natto in Japan, thua noa in
Thailand and kinema in India (Tamang, 1998). These are mainly used as culinary products to
enhance or intensify meatiness in soups, sauces and other prepared dishes.
The production of dawadawa involves extensive boiling and dehulling of the beans, followed by
further boiling to facilitate softening. Spontaneous fermentation of the softened beans is subsequently
allowed to take place over 24 days. Micro-organisms associated with the fermentation include
Bacillus subtilis (Ogbadu and Okagbue, 1988), B. pumilus (Ogbadu and Okagbue, 1988), B.
licheniformis (Ogbadu, Okagbue and Ahmad, 1990) and Staphylococcus saprophyticus (Odunfa,
1981). During the fermentation process, the pH increases from near neutral to approximately 8.0,
temperature increases from 25oC to 45oC and moisture increases from 43% to 56% (Odunfa and
Oyewole, 1986). At the same time, a five-fold increase in free amino acids takes place, and glutamate,
a flavour enhancer, increases five-fold during the process. Mechanisms of flavour production during
the fermentation process, as well as flavour principles generated during dawadawa fermentation
processing, have been studied by international food manufacturers and been used as a basis for the
development of flavours for incorporation in bouillon-type products (Beaumont, 2002).


C. Looking Forward: Preparing for the Future

5. A key issue in the sector where the application of biotechnologies could be useful
Emerging pathogens
The identification of infectious agents requires high-end technologies which are not usually available
in developing countries. Developing countries must, therefore, seek assistance from countries with
higher calibre technologies in order to characterize the infectious agents, put in place surveillance and
monitoring systems and develop strategies to contain the disease(s). Biotechnology can play a key role
in facilitating the characterization of new emerging pathogens. Traditional cultural methods for the
detection and enumeration of microbial pathogens are tedious and require at least 1218 hours for the
realization of results. By that time, the food products would have been distributed to retailers or
consumers. Immunoassay diagnostic kits facilitate near-real-time monitoring, sensitivity, versatility
and ease of use. The emergence of multi-antibiotic resistance traits is prevalent in intensive farming in
developing countries due to the abuse of antibiotics. The spread of multi-antibiotic resistant microorganisms poses public health concerns, because pathogens exhibiting such resistance would be
difficult to control with the use of currently available antibiotics. The rapid detection of these
pathogens, with high sensitivity, is one way of monitoring and containing the spread of multiantibiotic resistant traits. A strategic approach being employed by some is the development of affinity
biosensors with an antibiotic resistant nucleotide sequence as the detection probe.
6. Identifying options for developing countries
It is important that countries recognize the potential of fermented foods and prioritize actions to assure
their safety, quality and availability. Based on the stocktaking exercise in this document, a number of
specific options can be identified for developing countries to help them make informed decisions
regarding adoption of biotechnologies in food processing and in food safety for the future.
6.1 Regulatory and policy issues
Governments must be committed to protecting consumer health and interests, and to ensuring
fair practices in the food sector.
There has to be consensus at the highest levels of government on the importance of food
safety, and the provision of adequate resources for this purpose.
Government policy that is based on an integrated food-chain approach is science-based,
transparent and includes the participation of all the stakeholders from farm to table must be
put in place.
The importance of the regional and international dimensions of the use of biotechnologies in
food processing and safety must be recognized.
Priority must be accorded to promoting fermented foods in the food-security agendas of
Governments must also provide an enabling environment that is supportive of the growth and
development of upstream fermentation processes such as the production of high-value
fermented products, such as enzymes, functional-food ingredients and food additives.
6.2 International cooperation and harmonization
The organization and implementation of regional and international fora are critical
requirements for the enhancement of national organizational capability and performance and
for the facilitation of international co-operation. Further, the setting up of administrative
structures with clearly defined roles, responsibilities and accountabilities could efficiently
govern processed foods and safety issues.
Biotechnology-based Standard Operating Procedures (SOPs) for food safety should also be
documented for use in authorized laboratories.

National food control databases for the systematic collection, reporting and analysis of foodrelated data (food inspection, analysis, etc.) with set regulations and standards based on sound
science and in accordance with international recommendations (Codex) are key requirements.

6.3 Education policy

While the consumption of fermented foods is growing in popularity among higher-income
consumers thanks to increasing interest in wellness through diet, the consumption of
fermented foods by lower-income consumers in many developing countries is perceived to be
a backward practice.
o Strategies should therefore be developed for the dissemination of knowledge about
food biotechnology and, particularly, fermented foods. Targeted consumer education
on the benefits of consuming fermented food products and on applying good practice
in their production is required.
o Food biotechnology should be included in educational curricula in order to improve
the knowledge base in countries on the contribution of fermented foods to food and
nutritional security and to generate awareness of the growing market opportunities for
fermented foods and high-value products derived from fermentation processes.
6.4 Information-sharing
Access to specialized technical information on biotechnology and biotechnological
developments in the food processing sector are critical and necessary inputs and support
systems for guiding and orienting the research agendas of countries. The necessary
information systems should therefore be developed to facilitate rapid access to information on
biotechnological developments across both the developed and the developing world.
6.5 Legislation and policy on technologies
Expertise in legislation and technology licensing, as well as knowledge about how to nurture
innovation and turn it into business ventures, are critical requirements for developing
countries. Successful technology transfer requires all of these elements and an environment
that is conducive to innovation. Government policy in developing countries should therefore
prioritize technology transfer that helps create new business ventures, an approach that
requires government support such as tax incentives and infrastructure investment.
6.6 Intellectual property rights (IPR)
Many of the traditional fermentation processes applied in developing countries are based on
traditional knowledge. Enhanced technical and scientific information is required in order to
claim ownership of the traditional knowledge of the craft of indigenous fermented foods. Lack
of technical knowledge has resulted in the failure to realize the benefits of the industrialization
of indigenous fermented foods by individuals who are the rightful owners of the technology.

Greater focus is required on issues of relevance to IPR and on the characterization of

microbial strains involved in traditional fermentation processes. Emphasis must be placed on
IPR education for scientists. National governments should put in place the requisite
infrastructure for IPR to facilitate the process. At the institutional level, this infrastructure
would include technology management offices for assisting scientists in procedures relating to
intellectual property matters. The processes used in the more advanced areas of agricultural
biotechnology are generally covered by IPR, and the rights are generally owned by parties in
developed countries.
6.7 Communication and consumer perceptions
Communication between various stakeholders is critical in proactively engaging with
consumers. Communication must be established with the public at large on processed food
and associated hazards. Communication gradually builds confidence and will be critical to
advancing the application of biotechnologies in food processing and safety. The primary role

of communication in this respect is to ensure that information and opinions from all
stakeholders are incorporated in the discussion and decision-making process. The need for
specific standards or related texts and the procedures followed to determine them should also
be clearly outlined. The process, therefore, should be transparent.
o Public awareness and education are critical to the success of food bioprocessing and
food safety in developing countries.
o Greater attention must be directed toward understanding consumer and producer
(processor) perceptions on food safety and quality in developing countries.
o If foods are to be promoted as being safe and healthy, their nutritional and safety
attributes must be transparently demonstrated by presenting scientific data to
substantiate the nutritional and health benefits and by applying good
manufacturing/hygiene practice and HACCP as safety measures to ensure that issues
of consumer concern are addressed.
6.8 Technical capacities and technology transfer
Traditional fermented foods should be viewed as valuable assets. Governments should
capitalize on these assets and add value to them by supporting research, education and
development, while building on and developing the indigenous knowledge base on food
o Government agencies in developing countries should focus on the development of
technical capacities to deal with emerging technical issues.
o The technical capacities of academic and research institutes should be strengthened in
the fields of food biotechnology, food processing, bioprocess engineering and food
safety through training and exchange programmes for researchers. Such programmes
should emphasize collaboration with both developed and developing country
institutions engaged in work on food biotechnology, starter culture development,
bioprocess engineering and food safety.
o Training capabilities in food biotechnology and food safety should be developed
within developing country institutions through the introduction of degree courses in
order to broaden the in-country technical support base for food bioprocess
development. Given the similarities among fermentation processes across regions, an
inventory of institutions engaged in food biotechnology in developing countries would
be an asset in facilitating networking among institutions. Food processors, policymakers and equipment manufacturers should also be integrated into the networking
o The development of appropriate levels of bioreactor technology with control
bioprocess parameters will be necessary to improve the hygienic conditions of the
fermentation processes.
o Research and infrastructural development to enable the cost-effective production of
defined starter cultures in a stable format (i.e. cultures which do not require
refrigeration and have prolonged shelf-life under ambient conditions) should be
o Infrastructure development to facilitate the transfer and adaptation of fermentation
technologies developed at the laboratory level to the household and village and, where
necessary, the enterprise level should be prioritized.
o Appropriate levels of equipment will also be required to facilitate the downstream
processing of these products.
o Traceability systems that facilitate the differentiation and identification of food
products should be prioritized in order to broaden market opportunities for these
o A food-chain approach to assuring food safety should be prioritized by governments.

Food safety management systems should be strengthened by implementing systematic food

safety measures such as GHP, GMP and HACCP in food fermentation operations. Diagnostic

kits are important tools for monitoring and verifying the level of sanitation in processing
o Highly sensitive and rapid diagnostic kits are invaluable for monitoring and rapidly
detecting chemical and microbiological hazards that pose a threat to human health,
with high precision and sensitivity. The development of low-cost diagnostic kits
suitable for use by small processors would greatly facilitate food-safety monitoring.
Development should target the realization of multiplex diagnostic systems with the
capacity to detect several pathogens or many chemical contaminants using a single
diagnostic kit. The development of diagnostic kits at a national level could further
reduce their cost of production. Given the regional specificity of bacterial pathogens at
the species and subspecies levels, such diagnostic kits should be developed with
specificity and sensitivity to the species or subspecies that are prevalent in a specific
region. Investment is therefore needed for the development of expertise, facilities and
the infrastructure for the mass production of antibodies, cell culture technology and
for the formation of technical know-how on assembling the requisite components of
diagnostic kits.

The development of national hazard -profile databases that document the prevalent
pathogens in different regions will be critical. Such information would be useful for
further research into the development of diagnostic kits with high precision and
sensitivity and in implementing HACCP as well as risk assessment research. The
culture collection of identified infectious agents in the hazard profiles could play an
important role for specific antibody production for use in the development of
immunoassay diagnostic kits.

7. Identifying priorities for action for the international community

The last decade has witnessed considerable change with respect to the application of biotechnology in
food processing and food-safety applications. Market forces have been the major drivers of change in
the food sector of developing countries. Modern biotechnological tools are likely to play a greater role
in the development of efficient science-based processes for food processing and safety in order to
respond to consumer demand. The production of high-value fermented products such as enzymes,
functional food ingredients and food additives is likely to continue to increase in developing countries.
The international community (FAO, UN organizations, NGOs, donors and development agencies) can
play a major role in assisting developing countries to maximize the benefit to be derived from food
bioprocessing. The adoption of biotechnology-based methods in food processing and for food safety
and quality monitoring is dependent on several factors that include capacity-building in technical and
regulatory areas, policy formulation, regulatory frameworks and regional networks.
On the basis of analysis in this document, a number of priority areas to be supported by the
international community are presented below:
7.1 Capacity-building and human resource development
a) Support for basic and advanced education.
b) Prioritization of specific areas for investment.
c) Development of policies, priorities and action programmes that promote food fermentation as
a means of addressing food security.
d) Support for human resource development in a range of scientific disciplines food
biotechnology, food safety, bioengineering and enzyme technology.

e) Support for capacity-building initiatives for household-level, small- and medium-scale
processors of fermented foods.
f) Support for IPR development.
7.2 Technology transfer and support for research and development
a) Improvement of the relevance of national research to the needs of the food sector in
developing countries.
b) Enhancement of competitiveness and the creation of an enabling environment that is
conducive to private-sector investment in research, development and innovation for the
upgrading of food fermentation processes to respond to market demand.
c) Establishment and strengthening of the research and infrastructural support base for work on
starter culture development, bioreactor design and for the development of diagnostic equipment
for monitoring food safety and traceability. This infrastructural support base would include
laboratories, laboratory equipment, cell bank facilities for the proper preservation and storage of
microbial culture preparations.
d) Development of scientific data to substantiate the nutritional, health and health-benefit claims
associated with fermented foods.
e) Establishment of pilot processing facilities for the scale-up and testing of technologies
developed in order to facilitate their adoption.
7.3 Networking and clusters
a) Support for the development of regulatory frameworks for food safety.
b) Support for North-South and South-South training and exchange on food biotechnologies,
bioprocess engineering and food safety.
c) Promotion and facilitation of networking among scientists, researchers, small- and mediumscale food processors and the retail sector in order to facilitate knowledge and informationsharing.
d) Support for leveraging the traditional knowledge base in the upgrading of foodfermentation processing operations.


Table 1. Some methods employed in genetic research and the development of wine yeasts

Mutation and
Rare mating



Cannot generally be used directly, but the method is not entirely obsolete. Has been
used to study the genetic control of flocculation, sugar uptake and flavour production.
Cross-breeding and hybridization of spore-derived clones of S. cerevisiae have also
been accomplished.
For example, to induce autotrophic and de-repressed mutants for efficient sugar
fermentation and ethanol tolerance.
Mixing of non-mating strains at high cell density (ca. 108 cells/ml) results in a few true
hybrids with fused nuclei. Cytoduction (introduction of cytoplasmic elements without
nuclear fusion) can also be used to impart killer activity (using karyogamy deficient,
Kar-, mutants).
Spheroplasts from yeast strains of one species, the same genus, or different genera can
be fused to produce intraspecific, interspecific or intergeneric fusants, respectively. The
possibility exists to introduce novel characteristics into wine yeast strains which are
incapable of mating.
Transfer of whole chromosomes from wine trains (using the Kar- mutation) into
genetically defined strains of S. cerevisiae.
Introduction of genes from other yeasts and other organisms.

Source: Pretorius, 2000

- 23 -

Table 2. African fermented foods and their methods of inoculation - compiled from information obtained from Odunfa and Oyewole (1997).




Type of

Micro-organisms associated with the

fermentation process

Methods of

State of
development 2

Natural/ chance


Natural / chance






(A) Fermented starchy staples


West and

Solid state


West Africa



Lafun /

Corynebacterium mannihot, Geotrichum

species, Lactobacillus plantarium,
Lactobacillus buchnerri, Leuconsostoc
species, Streptococcus species.
Bacillus species, Lactobacillus species
such as Lactobacillus plantarum;
Leuconostoc mesenteroides;
Lactobacillus cellobiosus; Lactobacillus
brevis; Lactobacillus coprophilus;
Lactobacillus lactis; Leuconostoc lactis
and Lactobacillus bulgaricus, Klebsiella
species, Leuconostoc species,
Corynebacterium species and a yeast of
the Candida species.
Bacillus species, Klebsiella species,
Candida species, Aspergillus species;
Leuconostoc mesenteroides,
Corynebacterium manihot, Lactobacillus
plantarum, Micrococcus luteus and
Geotrichum candidum

West Africa

Corynebacterium, Bacillus,
Lactobacillus, Micrococcus,


Africa / Zaire

Solid state

State of development of each fermented product. It is the personal assessment of data, literature, internet search and other information by O.B. Oyewole as at March 2009.

- 24 -





East and

Type of

Micro-organisms associated with the

fermentation process
Pseudomonas, Acinetobacter and

Methods of

State of
development 2



Corynebacterium, Bacillus,
Lactobacillus, Micrococcus,
Solid state

(B) Gruels and beverages



West Africa /

Lactobacillus plantarum,
Corynebacterium specie, Aerobacter,
yeasts Candida mycoderma,
Saccharomyces cerevisiae and
Rhodotorula and molds Cephalosporium,
Fusarium, Aspergillus and Penicillium
Lactobacillus plantarum.




Solid state and

Leuconostoc mesenteroides,
Lactobacillus plantarum.



Koko/ Akasa
(C) Alcoholic beverages


Palm wine /

East Africa/

West Africa /

West Africa


Appropriate starters
produced by backslopping
Appropriate starters
produced by backslopping
Appropriate starters
produced by backslopping/inoculation




Enterobacter cloacae, Acinetobacter sp.,

Lactobacillus plantarum, L. brevis,
Saccharomyces cerevisiae, Candida
Solid state


Saccharomyces cerevisiae,
Schizosaccharomyces pombe,
Lactobacillus plantarum, L.
- 25 -







Various types
of African
cereal grains
Millet- used)


East Africa /

Type of

Micro-organisms associated with the

fermentation process







Natural / chance
Inoculation belt


Saccharomyc. cerevisiae,
Schizosaccharomyces pombe,
Lactobacillus plantarum, L.



Saccharomyces cerevisiae, S. chavelieri,
Candida sp and, Leuconostoc
meseteroides. Acetobacter sp.

West Africa

Geotrichum candidum, Lactobacillus sp.
and Candida sp.

West Africa
(D) Acid leavened bread/pancakes



Enjera / Tef
(E) Legumes - Condiments
Locus bean / Dawadawa/
West Africa
Etchum, Kal
Soumbara, Chu

State of
development 2

Saccharomyces cerevisiae,
Schizosaccharomyces pombe,
Lactobacillus plantarum, L.


Various types
of African
cereals grains

Methods of


Appropriate starters
produced by backslopping
Appropriate starters
produced by backslopping


Bacillus subtilis, B. pumilus, B.licheniformis
and Staphylococcus saprophyticus


- 26 -

African oil
Melon Seeds,
castor oil
bean, sesame
Cotton seed


Ogiri / Ogili



Type of

West, East and

Central Africa

West Africa

Micro-organisms associated with the

Methods of
fermentation process
Bacillus subtilis, B. pumilus, B.licheniformis
and Staphylococcus saprophyticus
Bacillus subtilis, B. pumilus, B.licheniformis,
Staphylococcus saprophyticus, Lactobacillus


Bacillus subtilis, B. pumilus, B.licheniformis,

Staphylococcus saprophyticus


State of
development 2


(F) Animal products

East and Central
North, East
Central Africa
Cow milk
Leben / Lben
Af i
**Key to codes for the state of development
1: Micro-organisms involved known
2: Roles of individual micro-organisms known
3: Genetic improvement carried on organisms.
4: Starter cultures available for the fermentation
5: Varieties of raw materials that are best suited for the product known
6: Improved technology available and adopted
7: Pilot Plant production
8: Industrial Plant production
If blank, then information is not available
Goat milk


Canida spp., Saccharomyces spp.,

Lactobacillus spp., Leuconostoc spp.,
Candida spp., Saccharomyces spp.,
Lactobacillus spp., Leuconostoc spp.,

- 27 -


Table 3. Examples of technologies used in indigenous fermented food production systems in Asia

Indigenous Country

Type of technology



Soy Sauce








Koji and

Aspergillus sp.



Aspergillus flavus
var columnaris

Viet Nam,
Lao and


Lactic Acid

- 28 -

Nature of
of starter
Solid Liquid Dry

Food safety
techniques used in
quality control and
quality assurance

ELISA for detection

of toxigenic fungi and
ELISA and/or GCMS to detect and/or
monitor carcinogens

1.Selective cultural
medium for pathogen

Table 4. Examples of fermented foods produced in Latin America

Black maize
Maize, manihot or
Maize or rice
Maize, yuca,
cassava, sweet
potatoes, Quinoa
or ripe plantains

Atole agrio


Micro-organisms associated


Bacillus spp., Aspergillus spp.,

Actinomycete spp. 1
Lactic acid bacteria





Colombia, Peru
Bolivia, Brazil,
Ecuador, Peru





Po de





Aguamiel (Agave
atrovirens and A.
Maize juice,
toasted maize and
pir fruits
Maize and red











"Pulque" syrup,
chili and toasted
maize leaves
Maize juice and
"pulque" or brown

Saccharomyces spp.,
Lactobacillus spp., Leuconostoc beverage
spp., Acetobacter spp.,
Aspergillus spp., Penicillium
Lactobacillus cellobiosus,
Streptococcus lactis,
Corynebacterium spp.
Lactobacillus spp., Leuconostoc
spp., Candida spp.,
Enterobacteriacea, Bacillus
cereus, Paracolobactrum
aerogenoides, Agrobacterium
azotophilum, Alkaligenes
pozolis, Escherichia coli var.
napolitana, Pseudomonas
mexicana, Klebsiella
pneumoniae, Saccharomyces
spp.and molds
Saccharomyces carbajali,
Lactobacillus plantarum,
Leuconostoc spp.

- 29 -


acidic beverage


Maize, pineapple,
apple or orange



Germinated maize
ground and
cooked with
fragments of






Maize beer and

zarzaparrilla bark

bark wine


Bacillus subtilis, B. graveolus

and the yeasts, Torulopsis
insconspicna, Saccharomyces
cerevisiae and Candida
Lactobacillus spp.,
Streptococcus spp.,
Leuconostoc spp., Pediococcus
spp., Saccharomyces spp.,
Candida spp., Cryptococcus
spp., Hansenula spp.,
Brettanomyces spp., Pichia
spp., Geotrichum spp. and
Penicillium spp.



Information adapted and modified from FAO (1998) and FAO (1999)
Information from Van Veen and Steinkraus (1970)
Information from Ray and Sivakumar (2009)


- 30 -

Table 5. Examples of some food additives and processing aids produced with the use of GM microorganisms.
Additive/processing aid

Organic acids
Amino acids

Amylase, isomerase
Citric acid
Benzoic, probionic acid
Methionine, lysine, tryptophan
Aspartic acid, phenylalanine

Low-calorie products

Aspartame, thaumatin, monellin

Modified fatty acids triglycerides

Microbial polysaccharides

Xanthan gum

Flavours and pigments

Single-cell protein

Vanillin, Monascin

High fructose corn syrup
Meat tenderizer
"Lite" beer
Food preservative
Nutritional supplement
Ingredient in sweetener
Non-nutritive sweeteners
Food additives
Cooking oil
Stabilizers, thickeners and gelling
Flavouring and colouring agents
Animal and human food

Table 6. Enzymes from GM micro-organisms

Source micro-organism
Aspergillus niger

Escherichia coli K-12

Fusarium venenatum
Kluyveromyces marxianus var. lactis
Pseudomonas fluorescens

Aspartic proteinase
Glucose oxidase
acetolactate decarboxylase
Maltogenic amlyase

Trichoderma reesei

Pectin lyase

Aspergillus oryzae

Bacillus licheniformis
Bacillus subtilis

Source: Extracted from Olempska-Beer et al., 2006.

- 31 -

Table 7. Biotechnologies applied in food safety assays in developing countries
Food production
I. Pre-processing of
incoming raw material
from producers (farms)

II. Processing
Raw material

III. Packaging and end

product analysis

Risk factor


-Improper practice

-Pesticide residues

-Presence of contaminants

-Heavy metals
-Undeclared additives
and supplements

-Improper handling

TLC (thin layer chromatography
GC (gas chromatography)


Some lower-middle and

middle- income


Low-, lower-middleand middleincome economies


Growth in culture media

-Quality parameters


Biochemical and enzyme assays

pH measurements

Contamination from
packaging material

-Undeclared allergens
and additives

TLC, GC, HPLC, fast protein liquid

-Pieces, fragments of

Biosensors for pesticides,
antibiotics, metals, antibiotics
and micro-organisms
ELISA for aflatoxins and
natural plant toxins

Country level

Atomic absorption spectrophotometry


-Fermentation procedures
involving micro-organisms

-Non-sterile conditions
leading to microbial


Growth in culture media

Mass spectrometry (MS)

methods for additives

indicator culture media
Antibody based biosensors
PCR detection of specific genes
Biosensing of fermentation
related enzymes
Monitoring of sugars, alcohol,
organic and inorganic ions
Surface plasmon resonance

- 32 -

Some lower-middle and


indicator culture media
PCR detection of specific
Metal detection systems

Inspection and sampling



Table 8. HACCP plan for the production of Nham (Paukatong and Kunawasen, 2001)
Process step


Critical limits




Weighing of

weight nitrite:
if the level too
high - chemical
hazard. If too
low may result

100 ppm <

initial nitrite
level < 200

Quality control
(QC) supervisor
random check the
nitrite according
to appropriate

reweighs every
bag of nitrite
since last
check, record
deviation Recalibrate the

Nitrite weighing
records Deviation
records Balance


Failure to
remove metal
contaminate in

No metal in

Line worker is to
visually inspect
each Nham
product during
stuffing and
change worker
every 30 minutes

Line worker
segregate metal
and record

inspection record any


Failure to
provide the
information to

Contain safety
such as safe
if cooked
on each Nham

Line worker
random visual
check the label
on Nham product

Line worker
recheck Nham
product since
check, label
product, and
record deviation

inspection Record any


resulting in
growth of

The pH of
Nham product
is lower than

QC worker
random monitor
pH of Nham in
every lot

QC worker
hold the prolong
and record

Monitoring pH
Records any

- 33 -

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E. Glossary of selected terms
Amplified Fragment Length Polymorphism (AFLP): Amplified fragment length polymorphism is a
novel molecular fingerprinting technique that can be applied to DNAs of any source or complexity.
Total genomic DNA is digested using two restriction enzymes. Double-stranded nucleotide adapters
are ligated to the DNA fragments to serve as primer binding sites for PCR amplification. Primers
complementary to the adapter and restriction site sequence, with additional nucleotides at the 3-end,
are used as selective agents to amplify a subset of ligated fragments. Polymorphisms are identified by
the presence or absence of DNA fragments following analysis on polyacrylamide gels. This technique
has been extensively used with plant DNA for the development of high-resolution genetic maps and
for the positional cloning of genes of interest. However, its application is rapidly expanding in bacteria
and higher eukaryotes for determining genetic relationships and for epidemiological typing.
Biosensor: is the self-contained analytical device that responds selectively and reversibly to the
concentration or activity of chemical species in biological samples using various types of sensors of
biological nature. Any sensor physically or chemically operated in biological samples can be
considered as biosensor.
Classical mutagenesis: The process involves the production of mutants through the exposure of
microbial strains to mutagenic chemicals or ultraviolet rays to induce changes in their genomes.
Improved strains thus produced are selected on the basis of specific properties such as improved
flavour-producing ability or resistance to bacterial viruses.
Conjugation: This is a natural process whereby genetic material is transferred among closely related
microbial species as a result of physical contact between the donor and the recipient micro-organisms.
Enzyme-Linked Immunosorbent Assay (ELISA): An immunoassay that uses specific antibodies to
detect antigens or antibodies in body fluids. The antibody-containing complexes are visualized
through enzymes coupled to the antibody. Addition of substrate to the enzyme-antibody-antigen
complex results in a coloured product.
Genomics: is the study of genes and their functions, and related technologies.
Hybridization: This is the common sexual breeding or mating process leading to genetic
recombination. Such sexual crossing has led to offspring with superior or improved qualities. For
example, the crossing of haploid yeast strains with excellent gassing properties and good drying
properties could yield a novel strain with both good gassing and drying properties.
Polymerase Chain Reaction (PCR): is a method to amplify DNA in vitro, involving the use of
oligonucleotide primers complementary to and annealing at different positions of nucleotide sequence
in a target gene. The copying of target sequences is by the action of DNA polymerase.
Probe: is a single-stranded nucleic acid that has been radio-labelled, and is used to identify a
complementary nucleic acid sequence that is membrane-bound.
Randomly Amplified Polymorphic DNA (RAPD): Randomly amplified polymorphic DNA and
arbitrarily primed PCR (AP-PCR) represent novel DNA polymorphism assays, sometimes referred to
as DNA fingerprinting, that involve the amplification of random DNA segments using PCR and
oligonucleotide primers of arbitrary sequence. Products defining the polymorphisms exhibit
Mendelian inheritance, and thus possess tremendous potential utility as genetic markers in a diverse
array of scientific disciplines.
Recombinant DNA Technology: This technology is the application of in vitro nucleic acid
techniques including recombinant deoxyribonucleic acid (DNA) and direct injection of nucleic acids
into cells and organelles (adapted from Codex CAD/GL 44-2003, CAD/GL 45-2003, CAD/GL 452003 and CAD/GL 68-2008)